Dear Loobosh,
NI-9403 has only digital I/O, so you can't use it for tasks requiring counters.
I don't really see an easy way to implement what you want. If you are using the module in a CompactRIO chassis, you would be able to design your own custom counter and perform those measurements on FPGA.
I also found an example that shows how you can use digital input to perform encoder measurements, but it also requires a counter for synchronization:
http://zone.ni.com/devzone/cda/epd/p/id/5753
Regards,